Merge pull request #1062 from griffithlab/pvacview_reviewer_response

pVACview reviewer response
griffithlab · May 8, 2024 · f8add9d · f8add9d
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diff --git a/...mages/screenshots/vignette/pvacview-aggrReportTable_withCGCgenesHighlighted.png b/...mages/screenshots/vignette/pvacview-aggrReportTable_withCGCgenesHighlighted.png
diff --git a/docs/images/screenshots/vignette/pvacview-export.png b/docs/images/screenshots/vignette/pvacview-export.png
diff --git a/docs/images/screenshots/vignette/pvacview-loadDemoDataset.png b/docs/images/screenshots/vignette/pvacview-loadDemoDataset.png
diff --git a/docs/images/screenshots/vignette/pvacview-mainviewDemodataset.png b/docs/images/screenshots/vignette/pvacview-mainviewDemodataset.png
diff --git a/docs/images/vaxrank_table.png b/docs/images/vaxrank_table.png
diff --git a/docs/pvacview.rst b/docs/pvacview.rst
@@ -21,6 +21,7 @@ decisions when deciding final peptide candidates for personalized cancer vaccine
    :glob:
 
    pvacview/prerequisites
-   pvacview/getting_started
-   pvacview/features
+   pvacview/pvacseq_module
+   pvacview/neofox_module
+   pvacview/custom_module
    pvacview/troubleshooting
diff --git a/docs/pvacview/custom_module.rst b/docs/pvacview/custom_module.rst
@@ -0,0 +1,51 @@
+.. image:: ../images/pVACview_logo_trans-bg_sm_v4b.png
+    :align: right
+    :alt: pVACview logo
+
+.. _custom_module:
+
+.. raw:: html
+
+  <style> .large {font-size: 90%; font-weight: bold} </style>
+  <style> .bold {font-size: 100%; font-weight: bold} </style>
+
+.. role:: large
+.. role:: bold
+
+Custom Module
+---------------
+
+The custom module boasts the most flexibility for viewing neoantigen candidate data, since there are no required features that
+are expected to be in the file.
+
+We provide three examples of neoantigen prediction pipeline output data:
+
+:large:`Vaxrank`
+
+Therapeutic vaccines targeting mutant tumor antigens (“neoantigens”) are an increasingly popular form of 
+personalized cancer immunotherapy. Vaxrank is a computational tool for selecting neoantigen vaccine peptides 
+from tumor mutations, tumor RNA data, and patient HLA type. Vaxrank is freely available on `github
+<www.github.com/openvax/vaxrank>`_ under the Apache 2.0 open source license and 
+can also be installed from the Python Package Index.
+
+:large:`NeoPredPipe`
+
+`NeoPredPipe (Neoantigen Prediction Pipeline) <https://github.com/MathOnco/NeoPredPipe>`_
+is offered as a contiguous means of predicting putative 
+neoantigens and their corresponding recognition potentials for both single and multi-region tumor samples. 
+This tool allows a user to process neoantigens predicted from single- or multi-region vcf files using ANNOVAR 
+and netMHCpan.
+
+:large:`antigen.garnish.2`
+
+Human and mouse ensemble tumor neoantigen prediction from SNVs and complex variants. 
+Immunogenicity filtering based on the Tumor Neoantigen Selection Alliance (TESLA).
+https://github.com/andrewrech/antigen.garnish
+
+.. toctree::
+   :maxdepth: 2
+   :glob:
+
+   custom_module/custom_upload
+   custom_module/custom_features
+
diff --git a/docs/pvacview/custom_module/custom_features.rst b/docs/pvacview/custom_module/custom_features.rst
@@ -0,0 +1,61 @@
+.. image:: ../../images/pVACview_logo_trans-bg_sm_v4b.png
+    :align: right
+    :alt: pVACview logo
+
+.. _custom_features:
+
+Custom Features
+---------------
+
+Overview of Neoantigen Features
+_______________________________
+
+The **Overview of Neantigen Features** table displays the groups of candidates as designated
+by the feature specified by the user. The top candidate of the group according to the sort by feature
+is shown in the table. To investigate the candidates within the group, click the ``Investigate`` button.
+
+
+.. figure:: ../../images/screenshots/pvacview-custom-maintable-neopredpipe.png
+            :width: 1000px
+            :align: left
+            :figclass: align-left
+
+            Features grouped by HLA and sorted by binding affinity
+
+Detailed Data
+_____________
+
+The **Detailed Data** table shows all the candidates within the group so that users can
+compare them to one another. This table will only display the features that are
+selected on the upload page.
+
+.. figure:: ../../images/screenshots/pvacview-custom-detaileddatatable-neopredpipe.png
+            :width: 1000px
+            :align: left
+            :figclass: align-left
+
+            Features grouped by HLA and sorted by binding affinity
+
+
+Dynamic Scatter Plot
+____________________
+
+The data can be further investigated by using the **Dynamic Scatter Plot** where users can choose any feature to be the X-axis, Y-axis,
+color, or size variable. The X and Y scale can be transformed and a range of values subsetted. The color represents the minimum
+and maximum values and can also be changed to any HEX value.
+
+To view information about different points on the plot simply mouse over individual points. Users can export the current scatter plot
+by using the camera icon at the top right corner of the plot.
+
+.. figure:: ../../images/screenshots/pvacview-custom-dynamicscatter-neopredpipe.png
+            :width: 1000px
+            :align: left
+            :figclass: align-left
+
+
+
+
+
+
+
+
diff --git a/docs/pvacview/custom_module/custom_upload.rst b/docs/pvacview/custom_module/custom_upload.rst
@@ -0,0 +1,80 @@
+.. image:: ../../images/pVACview_logo_trans-bg_sm_v4b.png
+    :align: right
+    :alt: pVACview logo
+
+.. _custom_upload:
+
+Custom Upload
+-------------
+
+Upload
+______
+
+After successfully launching pVACview by completing the :ref:`prerequisites <pvacview_prerequisites>` section,
+any neoantigen candidate data from a local directory can be uploaded in a tab-separated (tsv) file format.
+When uploading the file, users can then choose how to visualize the data by selecting which feature
+from the input they would like to use to group and sort candidates.
+
+The feature chosen to group by
+will allow users to explore candidates that are simliar to one another in a separate table. For example,
+to mimic the pVACseq module, users could choose to group by variant.
+
+The order of the candidates in each grouping is determined by the numeric feature chosen to sort by.
+For example, candidates within the pVACseq module are sorted by tier.
+
+Finally, users can select what features to display for each group of peptides.
+The default selection is all features.
+
+.. figure:: ../../images/screenshots/pvacview-custom-upload-vaxrank.png
+    :width: 1000px
+    :align: right
+    :alt: pVACview Upload
+    :figclass: align-left
+
+
+Visualize and Explore
+_____________________
+
+Upon choosing how to display your data, different aspects of the neoantigen candidates can be explored.
+
+.. figure:: ../../images/screenshots/pvacview-custom-tables-vaxrank.png
+    :width: 1000px
+    :align: right
+    :alt: pVACview Upload
+    :figclass: align-left
+
+There are three features that can be used to explore data:
+
+- **Overview of Neoantigen Features**
+
+  - Main table showcasing the top candidate of each grouping.
+
+- **Detailed Data**
+
+  - All candidates within the group being investigated ordered by the 'sort by' feature.
+
+- **Dynamic Scatter Plot**
+
+  - A scatter plot comparing multiple features simultaneously.
+  - Users can change axis features, color feature, and size feature. Users can also transform the data with natural log, log2, log10, and square root, adjust data range, and set different colors for minimum and maximum.
+
+
+Investigating Different Candidates
+**********************************
+
+To investigate a group of candidates, click the ``Investigate`` button in the appropriate row of the **Overview of Neoantigen Features** table.
+The **Detailed Data** table will be updated with detailed data for that group of candidates.
+
+.. figure:: ../../images/screenshots/pvacview-custom-investigate-vaxrank.png
+    :width: 1000px
+    :align: right
+    :alt: pVACview Upload
+    :figclass: align-left
+
+All candidates can be explored together using the **Dynamic Scatter Plot**. To identify a candidate of interest from the scatter plot, simple mouse-over the point of interest for the specific information about that candidate to be shown.
+
+.. figure:: ../../images/screenshots/pvacview-custom-dynamicscatter-vaxrank.png
+    :width: 1000px
+    :align: right
+    :alt: pVACview Upload
+    :figclass: align-left
diff --git a/docs/pvacview/neofox_module.rst b/docs/pvacview/neofox_module.rst
@@ -0,0 +1,23 @@
+.. image:: ../images/pVACview_logo_trans-bg_sm_v4b.png
+    :align: right
+    :alt: pVACview logo
+
+.. _neofox_module:
+
+Neofox Module
+---------------
+
+`NeoFox (NEOantigen Feature toolbOX) <https://neofox.readthedocs.io/en/latest/index.html>`_ 
+is a python package that annotates a 
+given set of neoantigen candidate sequences with relevant neoantigen features.
+The tool covers neoepitope prediction by MHC binding and ligand prediction,
+similarity/foreignness of a neoepitope candidate sequence, combinatorial
+features and machine learning approaches by running a wide range of published
+toolsets on the given input data.
+
+.. toctree::
+   :maxdepth: 2
+   :glob:
+
+   neofox_module/neofox_upload
+   neofox_module/neofox_features
diff --git a/docs/pvacview/neofox_module/neofox_features.rst b/docs/pvacview/neofox_module/neofox_features.rst
@@ -0,0 +1,56 @@
+.. image:: ../../images/pVACview_logo_trans-bg_sm_v4b.png
+    :align: right
+    :alt: pVACview logo
+
+.. _neofox_features:
+
+Neofox Features
+---------------
+
+Annotated Neoantigen Candidates Table
+_____________________________________
+
+The **Annotated Neoantigen Candidates** table is generated as output from NeoFox and includes many annotations based on published neoantigen features.
+Users can page through the candidates, sort by any feature, and select one or more candidates for further investgation. We have marked the
+features we find most informative with an asterisk.
+
+.. figure:: ../../images/screenshots/pvacview-neofox-maintable.png
+    :width: 1000px
+    :align: right
+    :alt: pVACview Upload
+    :figclass: align-left
+
+Comparative Violin Plots
+________________________
+
+Users can investigate how selected candidates relate to the the rest of the dataset using the **Comparative Violin Plots**. Users can select as many candidates
+as they would like which will then be highlighted in red in the violin plots. They can also select up to six features to view at a time. We have pre-selected
+five features which we found informative.
+
+.. figure:: ../../images/screenshots/pvacview-neofox-violin-two.png
+            :width: 1000px
+            :align: left
+            :figclass: align-left
+
+Dynamic Scatter Plot
+____________________
+
+Users can further investigate the data using the **Dynamic Scatter Plot** where they can choose any feature to be the X-axis, Y-axis,
+color, or size variable. The X and Y scale can be transformed and a range of values subsetted. The color represents the minimum
+and maximum values and can be changed to any HEX value.
+
+To view information about different points on the plot simply mouse over individual points. Users can export the current scatter plot
+by using the camera icon at the top right corner of the plot.
+
+.. figure:: ../../images/screenshots/pvacview-neofox-dynamic-scatter.png
+            :width: 1000px
+            :align: left
+            :figclass: align-left
+
+
+
+
+
+
+
+
diff --git a/docs/pvacview/neofox_module/neofox_upload.rst b/docs/pvacview/neofox_module/neofox_upload.rst
@@ -0,0 +1,76 @@
+.. image:: ../../images/pVACview_logo_trans-bg_sm_v4b.png
+    :align: right
+    :alt: pVACview logo
+
+.. _neofox_upload:
+
+NeoFox Upload
+---------------
+
+Upload
+______
+
+After successfully launching pVACview by completing the :ref:`prerequisites <pvacview_prerequisites>` section, users can now upload their data by browsing through
+local directories to load in a tab-separated (tsv) file generated by NeoFox.
+
+The one required file should end with the suffix ``_neoantigen_candidates_annotated.tsv``.
+The module expects all NeoFox annotated features to be in in the file but can also handle input files with additional annotations appended to the neoantigen candidates.
+
+.. figure:: ../../images/screenshots/pvacview-neofox-upload.png
+    :width: 1000px
+    :align: right
+    :alt: pVACview Upload
+    :figclass: align-left
+
+
+Visualize and Explore
+_____________________
+
+Data
+****
+
+Upon successfully uploading the correct data file, users can now explore the different aspects of their neoantigen candidates.
+
+.. figure:: ../../images/screenshots/pvacview-neofox-maintable.png
+    :width: 1000px
+    :align: right
+    :alt: pVACview Upload
+    :figclass: align-left
+
+There are three features that can be used to explore data:
+
+- **Annotated Neoantigen Candidates Table**
+
+  - Main table showcasing all candidates
+
+- **Comparative Violin Plots**
+
+  - Up to six violin plots showcasing spread of any NeoFox feature
+  - Pre-selected features are ones that we found most informative
+  - Selected candidate are shown in red
+
+- **Dynamic Scatter Plot**
+
+  - A scatter plot comparing multiple NeoFox features simultaneously
+  - Pre-selected features are ones that we found most informative
+  - Users can change axis features, color feature, and size feature. They can also transform the data with natural log, log2, log10, and square root, adjust data range, and set different colors for minimum and maximum.
+
+
+Investigating Different Variants
+********************************
+
+To investigate different candidates simple click one or more row from the **Annotated Neoantigen Candidates** table. The selected candidate(s) will be highlighted in red in the **Comparative Violin Plots**. Selecting a candidate does not affect the **Dynamic Scatter Plot**.
+
+.. figure:: ../../images/screenshots/pvacview-neofox-violinplots_selected.png
+    :width: 1000px
+    :align: right
+    :alt: pVACview Upload
+    :figclass: align-left
+
+Users can explore all candidates together using the **Dynamic Scatter Plot**. To identify a candidates of interest from the scatter plot, simple mouse-over the point of interest for the specific information about that candidate to be shown.
+
+.. figure:: ../../images/screenshots/pvacview-neofox-dynamicscatterplot_selected.png
+    :width: 1000px
+    :align: right
+    :alt: pVACview Upload
+    :figclass: align-left
diff --git a/docs/pvacview/prerequisites.rst b/docs/pvacview/prerequisites.rst
@@ -13,7 +13,7 @@
 .. role:: bold
 
 Prerequisites
----------------
+--------------
 
 In order to launch the pVACview R shiny application, you will need to have R/ R studio and a list of R packages correctly installed.
 Once launched, pVACview will require you to upload your corresponding input files for analysis. Alternatively, there is also a demo dataset that can be loaded to explore basic features of the app.
@@ -48,6 +48,9 @@ Additionally, there are a number of packages you will need to install in your R/
   install.packages("curl", dependencies=TRUE)
   install.packages("string", dependencies=TRUE)
   install.packages("shinycssloaders", dependencies=TRUE)
+  install.packages("plotly", dependencies=TRUE)
+  install.packages("shinyWidgets", dependencies=TRUE)
+  install.packages("colourpicker", dependencies=TRUE)
 
 Note that certain R packages may have further dependencies that require additional installation. If you are using R studio, these should be automatically installed for you during the respective package
 installation process. However, if you are using conda-based R, you may need to install them manually (usually by running ``install.packages(<package name>)``).

diff --git a/docs/pvacview/pvacseq_module.rst b/docs/pvacview/pvacseq_module.rst
@@ -0,0 +1,16 @@
+.. image:: ../images/pVACview_logo_trans-bg_sm_v4b.png
+    :align: right
+    :alt: pVACview logo
+
+.. _pvacseq_module:
+
+pVACseq Module
+==============
+
+.. toctree::
+   :maxdepth: 2
+   :glob:
+
+   pvacseq_module/pvacseq_upload
+   pvacseq_module/pvacseq_features
+   pvacseq_module/pvacseq_vignette